Sequence Logo - Logo Creation

Logo Creation

To create sequence logos, related DNA, RNA or protein sequences, or DNA sequences that have common conserved binding sites, are aligned so that the most conserved parts create good alignments. A sequence logo can then be created from the conserved multiple sequence alignment. The sequence logo will show how well residues are conserved at each position: the higher the number of residues, the higher the letters will be, because the better the conservation is at that position. Different residues at the same position are scaled according to their frequency. The height of the entire stack of residues is the information measured in bits. Sequence logos can be used to represent conserved DNA binding sites, where transcription factors bind.

The information content (y-axis) of position is given by:

for amino acids,

for nucleic acids,

where is the uncertainty (sometimes called the Shannon entropy) of position

Here, is the relative frequency of base or amino acid at position, and is the small-sample correction for an alignment of letters. The height of letter in column is given by

The approximation for the small-sample correction, is given by:

where is 4 for nucleotides, 20 for amino acids, and is the number of sequences in the alignment.